First of, I don't believe that Kenshin would have involve himself in politics like this and show himself in Tokyo wherein politicians are arguing among themselves. Second, I think Kenshin would have not allowed the gaijin to kill all those Samurais if he really was there watching him slaughter them one by one, because Kenshin, by this time, was saving lives already and it's against his vow to allow anyone to die in front of his eyes. I believe if he was there, he would have prevented the gaijin to kill them.

Katsura (in canon, at least) has a blot/b to account for on the other side... How many dead in Kenshin's fifteenth year of life? A hundred? What do we call the people who use child soldiers today? Still, one of our dearest friends joined the military at fourteen (back in the 40's) by lying about his age. Did anyone then worry about his innocence?